The son of a bookseller, John McI. McCarter was educated at the University of Edinburgh and trained for the Presbyterian ministry at New College. After his ordination, "he responded to a call to labour in Natal [South Africa] in connection with the Dutch Reformed Church." He had pastorates at Weenen, Ladysmith, and Ermelo for a total of thirteen years. In 1869, he wrote a book entitled The Dutch Reformed Church in South Africa. This was published in Edinburgh and Cape Town, and later in Amsterdam in a Dutch-language edition: Geschiedenis der Nederduitsche Gereformeerde Kerk in Zuid-Afrika.

McCarter returned to Scotland around 1875. After several years of missionary service there, he left for Canada. He was based in Nova Scotia before coming to the Miramichi in 1880. In January of that year, he spoke to the Newcastle Temperance Society on "Zululand." Before the Rev. William Aitken was inducted at Newcastle in June, he supplied for nine weeks at St James Church. He then accepted a call to Red Bank, where he was inducted in August.

A significant event during McCarter's pastorate was the dedication of St Philip's Church at Whitneyville on 31 October 1886, which made Red Bank officially a two-point charge. Since he remained as minister until April 1887, his was much the lengthiest Red Bank pastorate up to that date. He subsequently had charges at Métis, Que., and at Bearbrook and Navan in Ontario. Around 1895, he moved to Montreal, where he headed the Montreal Christian Mission to the Jews. He went back to Scotland in 1902 and became associated with a medical mission to the Jews in Edinburgh. He was survived in 1908 by his wife, Agnes Arnold, who had been "closely identified with his evangelistic work" for nearly forty years.